Mingyang Li

Yang Tan, Chen Liu, Jingyuan Gao et al.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Mingchen Li, Heng Fan, Song Fu et al.

Prompt privacy is crucial, especially when using online large language models (LLMs), due to the sensitive information often contained within prompts. While LLMs can enhance prompt privacy through text rewriting, existing methods primarily focus on document-level rewriting, neglecting the rich, multi-granular representations of text. This limitation restricts LLM utilization to specific tasks, overlooking their generalization and in-context learning capabilities, thus hindering practical application. To address this gap, we introduce DP-GTR, a novel three-stage framework that leverages local differential privacy (DP) and the composition theorem via group text rewriting. DP-GTR is the first framework to integrate both document-level and word-level information while exploiting in-context learning to simultaneously improve privacy and utility, effectively bridging local and global DP mechanisms at the individual data point level. Experiments on CommonSense QA and DocVQA demonstrate that DP-GTR outperforms existing approaches, achieving a superior privacy-utility trade-off. Furthermore, our framework is compatible with existing rewriting techniques, serving as a plug-in to enhance privacy protection. Our code is publicly available at github.com/ResponsibleAILab/DP-GTR.

Hanjing Zhou, Mingze Yin, Wei Wu et al.

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.